PLAZA 3.0 Monocots : Functional Clustering

Functional clusters

Species	Chromosome	Experiment	Cluster id	Cluster size	Number of genes	E-value
Arabidopsis thaliana	5	13	CH_ath_42	6	6	0.00000000000000297752
Brachypodium distachyon	Bd1	13	CH_bdi_162	4	5	0.000000227838
Brachypodium distachyon	Bd3	13	CH_bdi_40	6	7	0.000000000000339648
Brachypodium distachyon	Bd3	13	CH_bdi_137	4	4	0.0000000456076
Oryza sativa ssp. indica	Chr02	13	CH_osaindica_159	6	16	0.0000000000120735
Oryza sativa ssp. indica	Chr03	13	CH_osaindica_262	5	14	0.00000000598516
Oryza sativa ssp. japonica	2	13	CH_osa_131	6	13	0.00000000000299464
Oryza sativa ssp. japonica	3	13	CH_osa_93	6	7	0.0000000000000122487
Physcomitrella patens	scaffold_33	13	CH_ppa_97	3	5	0.000324702
Physcomitrella patens	scaffold_48	13	CH_ppa_38	4	11	0.0000102323
Setaria italica	scaffold_1	13	CH_sit_328	5	22	0.000000858237
Setaria italica	scaffold_9	13	CH_sit_281	4	5	0.000000177371
Setaria italica	scaffold_9	13	CH_sit_20	9	9	1.80038e-23
Solanum lycopersicum	ch03	13	CH_sly_108	6	9	0.000000000000347342
Sorghum bicolor	chr_1	13	CH_sbi_53	7	7	6.85149e-17
Sorghum bicolor	chr_1	13	CH_sbi_443	3	3	0.0000540794
Sorghum bicolor	chr_4	13	CH_sbi_56	9	25	1.31005e-16
Sorghum bicolor	chr_7	13	CH_sbi_637	3	5	0.000539866
Zea mays	1	13	CH_zma_153	4	5	0.000000156833
Zea mays	1	13	CH_zma_464	3	5	0.000346243
Zea mays	5	13	CH_zma_54	7	25	0.00000000000930132
Zea mays	6	13	CH_zma_63	7	34	0.0000000001034

Exp id	Data type	Data filter	Min genes cluster	Max genes cluster	Max cluster size	E-value	Tandems removal
1	GO	Primary GO data only.	2	30	80	0.001	X
2	GO	Primary and orthology projected GO data.	2	30	80	0.001	X
3	GO	All GO data.	2	30	80	0.001	X
4	GO	Primary GO data only.	10	150	300	0.001	X
5	GO	Primary and orthology projected GO data.	10	150	300	0.001	X
6	GO	All GO data.	10	150	300	0.001	X
7	GO	Primary GO data only.	2	30	80	0.001	V
8	GO	Primary and orthology projected GO data.	2	30	80	0.001	V
9	GO	All GO data.	2	30	80	0.001	V
10	GO	Primary GO data only.	10	150	300	0.001	V
11	GO	Primary and orthology projected GO data.	10	150	300	0.001	V
12	GO	All GO data.	10	150	300	0.001	V
13	InterPro	No filter applied.	2	30	80	0.001	X
14	InterPro	No filter applied.	10	150	300	0.001	X
15	InterPro	No filter applied.	2	30	80	0.001	V
16	InterPro	No filter applied.	10	150	300	0.001	V
17	MapMan	No filter applied.	2	30	80	0.001	X
18	MapMan	No filter applied.	10	150	300	0.001	X
19	MapMan	No filter applied.	2	30	80	0.001	V
20	MapMan	No filter applied.	10	150	300	0.001	V